Did you measure out your batter? Perhaps one had a bit more than the other. If the pans were on the same rack, you shouldn't need to move them. If they arn't, than I would definatly switch them half way through.

I'm afraid I don't have an answer for your problem, but I recently switched from metal skewers to bamboo skewers (since they're longer than toothpicks) because I felt that they were giving me false "doneness" when I was testing. Since I switched to wooden, I feel more confident that my baked goods are getting done properly.

I'm not sure, but I think it's probably a live with it problem. Most ovens have a hot spot, you just have to figure out where it is. For me it's the bottom left rear corner. Things that I put in that spot tend to bake faster and more unevenly, so I have to be careful to rotate the pans. It probably has something to do with where the heating element in the stove is located. Mine has a sealed bottom so I can't see for sure, but that would be my guess.

A great way to test for hot spots is to line a cookie sheet with bread, then bake it (or broil it) until the bread toasts. You may end up with some bread still pale while other parts are burned, but at least you'll know what's happening where.